MDTAP

MDTAP automatically detects permeation events across membrane-embedded protein and nucleic acid channels from molecular dynamics simulation trajectories.

Key Features:

• Automated Permeation Detection: MDTAP automatically identifies and characterizes permeation events of any molecular type across any channel from MD simulation data.
• Multi-Format Trajectory Support: The tool accepts trajectories in DCD (CHARMM/NAMD) and PDB format obtained from any MD simulation package.
• Heterogeneous System Analysis: MDTAP can analyze permeation across heterogeneous lipid membranes and artificial nucleic acid channels.
• Bash-Based Analysis: The tool employs bash scripts to analyze input trajectories and characterize molecular permeation.

Scientific Applications:

• Membrane Protein Transport Studies: MDTAP enables analysis of solute, solvent, and drug molecule transport across protein channels embedded in membrane bilayers, as demonstrated with Escherichia coli outer membrane protein Wzi and E. coli Aquaporin Z.
• Nucleic Acid Channel Analysis: The tool supports permeation studies through artificial nucleic acid channels.
• Complex Lipid Membrane Systems: MDTAP addresses permeation across heterogeneous lipid membranes of growing biological importance.

Methodology:

MDTAP employs bash scripts to analyze DCD and PDB format trajectories to characterize molecular permeation events across channels.